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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 3-132705783-CCTT-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=132705783&ref=CCTT&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 132705783,
"ref": "CCTT",
"alt": "C",
"effect": "disruptive_inframe_deletion",
"transcript": "ENST00000337331.10",
"consequences": [
{
"aa_ref": "EG",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "c.1304_1306delAAG",
"hgvs_p": "p.Glu435del",
"transcript": "NM_153240.5",
"protein_id": "NP_694972.3",
"transcript_support_level": null,
"aa_start": 435,
"aa_end": null,
"aa_length": 1330,
"cds_start": 1304,
"cds_end": null,
"cds_length": 3993,
"cdna_start": 1360,
"cdna_end": null,
"cdna_length": 5348,
"mane_select": "ENST00000337331.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "EG",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "c.1304_1306delAAG",
"hgvs_p": "p.Glu435del",
"transcript": "ENST00000337331.10",
"protein_id": "ENSP00000338766.5",
"transcript_support_level": 1,
"aa_start": 435,
"aa_end": null,
"aa_length": 1330,
"cds_start": 1304,
"cds_end": null,
"cds_length": 3993,
"cdna_start": 1360,
"cdna_end": null,
"cdna_length": 5348,
"mane_select": "NM_153240.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "n.1010_1012delAAG",
"hgvs_p": null,
"transcript": "ENST00000465756.5",
"protein_id": "ENSP00000419907.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3852,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "n.*747_*749delAAG",
"hgvs_p": null,
"transcript": "ENST00000469232.5",
"protein_id": "ENSP00000418664.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1616,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP3-ACAD11",
"gene_hgnc_id": 48351,
"hgvs_c": "n.1304_1306delAAG",
"hgvs_p": null,
"transcript": "ENST00000471702.2",
"protein_id": "ENSP00000419763.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7784,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "n.538_540delAAG",
"hgvs_p": null,
"transcript": "ENST00000476742.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 650,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "n.1080_1082delAAG",
"hgvs_p": null,
"transcript": "ENST00000490993.5",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5197,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "n.1010_1012delAAG",
"hgvs_p": null,
"transcript": "ENST00000684294.1",
"protein_id": "ENSP00000508078.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3872,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP3-ACAD11",
"gene_hgnc_id": 48351,
"hgvs_c": "n.1408_1410delAAG",
"hgvs_p": null,
"transcript": "NR_037804.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7788,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "n.*747_*749delAAG",
"hgvs_p": null,
"transcript": "ENST00000469232.5",
"protein_id": "ENSP00000418664.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1616,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"dbsnp": "rs1456714047",
"frequency_reference_population": 0.0000033116573,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000294622,
"gnomad_genomes_af": 0.00000657263,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0.25999999046325684,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 6.606,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.26,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PM4_Supporting,PP5",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PM4_Supporting",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000337331.10",
"gene_symbol": "NPHP3",
"hgnc_id": 7907,
"effects": [
"disruptive_inframe_deletion"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1304_1306delAAG",
"hgvs_p": "p.Glu435del"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000471702.2",
"gene_symbol": "NPHP3-ACAD11",
"hgnc_id": 48351,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1304_1306delAAG",
"hgvs_p": null
}
],
"clinvar_disease": "Joubert syndrome and related disorders,NPHP3-related Meckel-like syndrome,Nephronophthisis,Nephronophthisis 3,Renal-hepatic-pancreatic dysplasia 1,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:3 US:1",
"phenotype_combined": "Nephronophthisis|Joubert syndrome and related disorders|Renal-hepatic-pancreatic dysplasia 1;NPHP3-related Meckel-like syndrome;Nephronophthisis 3|not provided",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}